TAM: a method for enrichment and depletion analysis of a microRNA category in a list of microRNAs.
TAM: a method for enrichment and depletion analysis of a microRNA category in a list of microRNAs.
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DOI：
10.1186/1471-2105-11-419
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发表时间：
2010-08-09
影响因子：
3
通讯作者：
Cui Q
中科院分区：
文献类型：
--
作者：
Lu M;Shi B;Wang J;Cao Q;Cui Q
microRNAs（miRNAs）是一类重要的基因调控因子。近年来，已鉴定的miRNAs的数量急剧增加。一个新出现的主要挑战是基因组规模的miRNA数据集的解释，包括来自微阵列和深度测序的数据集。了解一系列miRNA（即由miRNA微阵列或深度测序实验产生的去调控的miRNA）背后的共同规则或模式是有趣和重要的。为此，本研究提出了一种方法，并开发了一个工具（TAM）的注释有意义的人类miRNAs类别。我们首先根据已有的知识将miRNA整合到各种有意义的类别中，如miRNA家族、miRNA簇、miRNA功能、miRNA相关疾病和组织特异性。使用TAM，可以根据整合的miRNA分类数据快速注释和总结给定的miRNA列表。此外，给定一系列miRNAs，TAM可用于预测新的相关miRNAs。最后，我们通过两个独立的实验将TAM应用于急性心肌梗死（AMI）中失调的miRNAs，证实了TAM的有用性和可靠性。TAM可以有效地识别给定miRNA的有意义的类别。此外，TAM可用于鉴定新的miRNA生物标志物。TAM工具、源代码和miRNA类别数据可在http://cmbi.bjmu.edu.cn/tam上免费获得。
MicroRNAs (miRNAs) are a class of important gene regulators. The number of identified miRNAs has been increasing dramatically in recent years. An emerging major challenge is the interpretation of the genome-scale miRNA datasets, including those derived from microarray and deep-sequencing. It is interesting and important to know the common rules or patterns behind a list of miRNAs, (i.e. the deregulated miRNAs resulted from an experiment of miRNA microarray or deep-sequencing). For the above purpose, this study presents a method and develops a tool (TAM) for annotations of meaningful human miRNAs categories. We first integrated miRNAs into various meaningful categories according to prior knowledge, such as miRNA family, miRNA cluster, miRNA function, miRNA associated diseases, and tissue specificity. Using TAM, given lists of miRNAs can be rapidly annotated and summarized according to the integrated miRNA categorical data. Moreover, given a list of miRNAs, TAM can be used to predict novel related miRNAs. Finally, we confirmed the usefulness and reliability of TAM by applying it to deregulated miRNAs in acute myocardial infarction (AMI) from two independent experiments. TAM can efficiently identify meaningful categories for given miRNAs. In addition, TAM can be used to identify novel miRNA biomarkers. TAM tool, source codes, and miRNA category data are freely available at http://cmbi.bjmu.edu.cn/tam.
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人类microRNA和疾病关联的分析。
影响因子：
3.7
作者：
Lu, Ming;Zhang, Qipeng;Deng, Min;Miao, Jing;Guo, Yanhong;Gao, Wei;Cui, Qinghua
通讯作者：
Cui, Qinghua
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
DOI：
10.1073/pnas.0805038105
发表时间：
2008-09-02
影响因子：
11.1
作者：
van Rooij, Eva;Sutherland, Lillian B.;Olson, Eric N.
通讯作者：
Olson, Eric N.
影响因子：
14.9
作者：
Altuvia Y;Landgraf P;Lithwick G;Elefant N;Pfeffer S;Aravin A;Brownstein MJ;Tuschl T;Margalit H
通讯作者：
Margalit H
影响因子：
3.7
作者：
Alexiou P;Maragkakis M;Papadopoulos GL;Simmosis VA;Zhang L;Hatzigeorgiou AG
通讯作者：
Hatzigeorgiou AG